Half of the secondary teachers who responded to a survey on the senior phase of Curriculum for Excellence say their schools have adopted a traditional 2+2+2 curriculum structure - contrary to government guidance.
And 3 per cent of respondents to the poll by the Scottish Secondary Teachers' Association don't know which model their schools are opting for.
The findings will fuel the controversy raging over whether schools must adopt the government's favoured 3+3 structure - in which pupils only make their exam subject choices at the end of S3, following three years of the "broad general education" outlined in CfE guidance - or whether they can opt for the more traditional 2+2+2 model, deciding at the end of S2.
The survey of SSTA school reps, carried out over the past two weeks, had a return rate of 40 per cent by midday on Wednesday (it was due to close later in the day). At that point, 45 per cent said pupils in their school were making their subject choices at the end of S2; 46 per cent said they were making them at the end of S3; 10.7 per cent were choosing at the end of S1; and 54 per cent said the majority of their pupils were starting work on National 4 courses in S3, while 31 per cent said this would happen in S4.
Education secretary Michael Russell and Education Scotland's chief executive, Bill Maxwell, have insisted in statements and correspondence in recent weeks that the 2+2+2 model does not match their view of how CfE should be delivered in secondary schools.
"We are fully on track to deliver Curriculum for Excellence and have made clear that Education Scotland are on hand to address any concerns that schools may have regarding its ongoing rollout. Their chief executive has written out to all authorities to ensure the availability of this support is widely understood," said a government spokesman.
Mr Russell told TESS this week: "There is widespread support (in schools) for the model that is being supported nationally and that is what will be implemented. One local authority (East Renfrewshire) has chosen to do something different because it is coming from a different starting point."
Of schools who have not adopted the 3+3 model, he said: "I would hope they are listening very carefully to the advice and assistance they are getting - advice from HMIE - so they can ensure that the advantages of CfE are being delivered."
He insisted, however: "I am not imposing anything. This is a very longstanding agreement which everybody has signed up to - trade unions, every organisation on the management board, and every political party."
The SSTA findings suggest that substantially higher numbers of schools have opted to play it safe in the meantime and allow pupils to choose eight or nine courses at the end of S2, which they will then study over two years - S3-4 - before completing the new National 4 and 5 courses in 2013-14.
Ann Ballinger, general secretary of the SSTA, said that the most worrying figure was the 3 per cent who still did not know which model their school had chosen.
She also warned that it would be "chaotic" if schools which had chosen one model were made to switch to another at this stage.
"Perhaps the solution is to go back to the ethos of Curriculum for Excellence and allow schools to decide what is best for them and their pupils," she said; imposition was not what CfE was supposed to be about.
A spokesman for Education Scotland said the organisation was embarking on a programme of checking with every authority on the progress made by every school towards CfE implementation.
"Once we have that information we will know the real situation we are in," he said.